7.3 Translation Essential idea: Information transferred from DNA to mRNA is translated into an amino acid sequence. The image shows a table used to translate mRNA codons (which have been transcribed from DNA) into amino acids. "The genes in DNA encode protein molecules, which are the "workhorses" of the cell, carrying out all the functions necessary for life ... In the simplest sense, expressing a gene means manufacturing its corresponding protein" http://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393 By Chris Paine https://bioknowledgy.weebly.com/ https://commons.wikimedia.org/wiki/File:Aminoacids_table.svg

Understandings Statement Guidance 7.3.U1 Initiation of translation involves assembly of the components that carry out the process. Examples of start codons are not required. Names of the tRNA binding sites are expected as well as their roles. 7.3.U2 Synthesis of the polypeptide involves a repeated cycle of events.   7.3.U3 Disassembly of the components follows termination of translation. Examples of stop codons are not required. 7.3.U4 Free ribosomes synthesize proteins for use primarily within the cell. 7.3.U5 Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes. 7.3.U6 Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane. 7.3.U7 The sequence and number of amino acids in the polypeptide is the primary structure. 7.3.U8 The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. 7.3.U9 The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups. Polar and non-polar amino acids are relevant to the bonds formed between R groups. 7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain. Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein.

Applications and Skills Statement Guidance 7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.   7.3.S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes. 7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.

Review: 2.7.U4 Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase. AND 2.7.U5 Translation is the synthesis of polypeptides on ribosomes. http://learn.genetics.utah.edu/content/molecules/transcribe/

Review: 2.7.U5 Translation is the synthesis of polypeptides on ribosomes. Translation is the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain A ribosome is composed of two halves, a large and a small subunit. During translation, ribosomal subunits assemble together like a sandwich on the strand of mRNA: Each subunit is composed of RNA molecules and proteins The small subunit binds to the mRNA The large subunit has binding sites for tRNAs and also catalyzes peptide bonds between amino acids http://www.nature.com/scitable/topicpage/ribosomes-transcription-and-translation-14120660

Use this slide and the previous one to construct your own diagram. Review: 2.7.U5 Translation is the synthesis of polypeptides on ribosomes. (plus AHLdetail) To understand how ribosomes work learn how to draw, label and annotate their structure. Use this slide and the previous one to construct your own diagram. tRNA carrying amino acids bind first in this site. tRNA currently holding the growing peptide is located at this site tRNAs leave the ribosome at this site http://old-www.hartnell.edu/tutorials/biology/images/ribosome_sm.jpg http://www.proteinsynthesis.org/wp-content/uploads/2013/02/protein-synthesis-ribosome.jpg

7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.

7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.

They consist of a large and small subunit: 7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule. Ribosomes Ribosomes are made of protein (for stability) and ribosomal RNA (for catalytic activity) They consist of a large and small subunit: The small subunit contains an mRNA binding site The large subunit contains three tRNA binding sites – an aminoacyl (A) site, a peptidyl (P) site and an exit (E) site Ribosomes can be found either freely floating in the cytosol or bound to the rough ER (in eukaryotes) Ribosomes differ in size in prokaryotes and eukaryotes (prokaryotes = 70S ; eukaryotes = 80S)  

7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation. The binding of an amino acid to the tRNA acceptor stem occurs as a result of a two-step process: The enzyme binds ATP to the amino acid to form an amino acid–AMP complex linked by a high energy bond (PP released) The amino acid is then coupled to tRNA and the AMP is released – the tRNA molecule is now “charged” and ready for use The function of the ATP (phosphorylation) is to create a high energy bond that is transferred to the tRNA molecule This stored energy will provide the majority of the energy required for peptide bond formation during translation http://www.ib.bioninja.com.au/_Media/trna_activation_med.jpeg

7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation. The energy in the bond linking the tRNA molecule to the amino acid will be used in translation to form a peptide bond between adjacent amino acids http://www.ib.bioninja.com.au/_Media/trna_activation_med.jpeg

Review: 2.7.U7 Codons of three bases on mRNA correspond to one amino acid in a polypeptide. The genetic code is the set of rules by which information encoded in mRNA sequences is converted into proteins (amino acid sequences) by living cells Codons are a triplet of bases which encodes a particular amino acid As there are four bases, there are 64 different codon combinations (4 x 4 x 4 = 64) The codons can translate for 20 amino acids Different codons can translate for the same amino acid (e.g. GAU and GAC both translate for Aspartate) therefore the genetic code is said to be degenerate The order of the codons determines the amino acid sequence for a protein The coding region always starts with a START codon (AUG) therefore the first amino acid in all polypeptides is Methionine The coding region of mRNA terminates with a STOP codon - the STOP codon does not add an amino acid – instead it causes the release of the polypeptide Amino acids are carried by transfer RNA (tRNA) The anti-codons on tRNA are complementary to the codons on mRNA based on

Review: 2.7.U8 Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA. Key components of translation that enable genetic code to synthesize polypeptides tRNA molecules have an anticodon of three bases that binds to a complementary codon on mRNA tRNA molecules carry the amino acid corresponding to their codon 2 3 mRNA has a sequence of codons that specifies the amino acid sequence of the polypeptide 4 Ribosomes: act as the binding site for mRNA and tRNA catalyse the peptide bonds of the polypeptide 1 https://upload.wikimedia.org/wikipedia/commons/0/0f/Peptide_syn.png

The process of translation can be summarised by the following steps: 7.3.U1 Initiation of translation involves assembly of the components that carry out the process. AND 7.3.U2 Synthesis of the polypeptide involves a repeated cycle of events. AND 7.3.U3 Disassembly of the components follows termination of translation. The process of translation can be summarised by the following steps: initiation mRNA binds to the small subunit of the ribosome. The small subunit of the ribosome moves along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG) A molecule of tRNA (with it’s amino acid, Methionine attached) complementary to the start codon (UAC) binds to the P site of the ribosome The large subunit of the ribosome binds to the tRNA and small subunit A second tRNA (with amino acid attached) complementary to the second codon on the mRNA then binds to the A site of the ribosome The amino acid carried by the tRNA in the P site is transferred to the amino acid in the A site as a consequence of the ribosome catalyzing a new peptide bond (condensation reaction). The growing polypeptide increases in length. The ribosome moves one codon along the mRNA (in a 5’ – 3’ direction): The tRNA in the P site is moved to the E site and then released The tRNA in the A site is moved into P site Another tRNA binds, complementary to the next codon on the mRNA, binds to the A site. Steps 6, 7, and 8 are repeated until a stop codon is reached. When a stop codon is reached translation is stopped: a release factor attaches to the A site the polypeptide chain is released the ribosome complex dissembles ready for reuse translating another mRNA molecule elongation termination

7.3.U1 Initiation of translation involves assembly of the components that carry out the process. Note: a maximum of two tRNAs can be bound at the same time. mRNA binds to the small subunit of the ribosome. The small subunit of the ribosome moves along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG) A molecule of tRNA (with it’s amino acid, Methionine attached) complementary to the start codon (UAC) binds to the P site of the ribosome n.b. the A, P, E notation, though not necessary makes the process of translation easier to explain The large subunit of the ribosome binds to the tRNA and small subunit http://www.hartnell.edu/tutorials/biology/translation.html

7.3.U2 Synthesis of the polypeptide involves a repeated cycle of events. Elongation: A second tRNA (with amino acid attached) complementary to the second codon on the mRNA then binds to the A site of the ribosome The amino acid carried by the tRNA in the P site is transferred to the amino acid in the A site as a consequence of the ribosome catalyzing a new peptide bond (condensation reaction). The growing polypeptide increases in length. The ribosome moves one codon along the mRNA (in a 5’ – 3’ direction): The tRNA in the P site is moved to the E site and then released The tRNA in the A site is moved into P site Another tRNA binds, complementary to the next codon on the mRNA, binds to the A site. Steps 6, 7, and 8 are repeated until a stop codon is reached. http://www.hartnell.edu/tutorials/biology/translation.html

7.3.U3 Disassembly of the components follows termination of translation. When a stop codon is reached translation is stopped: a release factor attaches to the A site the polypeptide chain is released the ribosome complex dissembles ready for reuse translating another mRNA molecule http://www.hartnell.edu/tutorials/biology/translation.html

Translation can occur immediately after transcription in prokaryotes. 7.3.U6 Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane. Translation can occur immediately after transcription in prokaryotes. Growing polypeptide chain In prokaryotes ribosomes can be adjacent to the chromosomes whereas in eukaryotes the mRNA needs to be relocated from the nucleus to the cytoplasm (through the nuclear membrane) In eukaryotes the mRNA is modified, e.g. spliced, (here labelled processing) after transcription before translation, this does not occur in prokaryotes http://barleyworld.org/sites/default/files/figure-08-01_0.jpg

7.3.S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes. A polysome is a structure that consists of multiple ribosomes attached to a single mRNA Multiple ribosomes translating mRNA simultaneously enables the cell to quickly create many copies of the required polypeptide. Electron micrograph showing a polysome Diagram of a generalised polysome http://urei.bio.uci.edu/~hudel/bs99a/lecture21/polysome.gif

7.3.S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes. In prokaryotes the chromosome may have numerous polysomes attached directly to it. Features to take note of: The arrow indicates the chromosome Polysomes show as the side chains. The dark ball-like ribosomes on each polysome side chain are clearly visible Electron micrograph showing growing polysomes on a chromosome from E. coli. n.b. polysomes in eukaryotes occur separately in the cytoplasm or on the ER. This is because Ribosomes attach to the mRNA as it is being translated. http://www.nature.com/scitable/content/27459/williams_polysome_mid_1.jpg

Q - What is the purpose of transcription and translation? Review: 2.7.U4 Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase. AND 2.7.U5 Translation is the synthesis of polypeptides on ribosomes. Q - What is the purpose of transcription and translation? A - These processes work together to create a polypeptide which in turns folds to become a protein. Proteins carry many essential functions in cells. For more detail review 2.4.U7 Living organisms synthesize many different proteins with a wide range of functions. Catalysis Tensile strengthening Transport of nutrients and gases Cell adhesion Muscle contraction Use the learn.genetics tutorial to discover one example: Hormones Receptors Cytoskeletons Packing of DNA Blood clotting Immunity Membrane transport http://learn.genetics.utah.edu/content/molecules/firefly/

Review: 2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.

Review: 2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. Proteins are commonly described as either being fibrous or globular in nature. Fibrous proteins have structural roles whereas globular proteins are functional (active in a cell’s metabolism). In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from the surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R groups are exposed and therefore the molecule is insoluble.

7.3.U7 The sequence and number of amino acids in the polypeptide is the primary structure. AND 7.3.U8 The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. AND 7.3.U9 The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups. AND 7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain. There are four levels of protein structure. Which level a protein conforms to is determined by it’s amino acid sequence. (Polypeptide) The order / sequence of the amino acids of which the protein is composed Formed by covalent peptide bonds between adjacent amino acids Controls all subsequent levels of structure The chains of amino acids fold or turn upon themselves Held together by hydrogen bonds between (non-adjacent) amine (N-H) and carboxylic (C-O) groups H-bonds provide a level of structural stability Fibrous proteins The polypeptide folds and coils to form a complex 3D shape Caused by interactions between R groups (H-bonds, disulphide bridges, ionic bonds and hydrophilic / hydrophobic interactions) Tertiary structure may be important for the function (e.g. specificity of active site in enzymes) Globular proteins The interaction between multiple polypeptides or prosthetic groups A prosthetic group is an inorganic compound involved in a protein (e.g. the heme group in haemoglobin) Fibrous and Globular proteins

Primary (1º) Structure The first level of structural organisation in a protein is the order / sequence of amino acids which comprise the polypeptide chain The primary structure is formed by covalent peptide bonds between the amine and carboxyl groups of adjacent amino acids Primary structure controls all subsequent levels of protein organisation because it determines the nature of the interactions between R groups of different amino acids

Secondary (2º) Structure The secondary structure is the way a polypeptide folds in a repeating arrangement to form α-helices and β-pleated sheets This folding is a result of hydrogen bonding between the amine and carboxyl groups of non-adjacent amino acids Sequences that do not form either an alpha helix or beta-pleated sheet will exist as a random coil Secondary structure provides the polypeptide chain with a level of mechanical stability (due to the presence of hydrogen bonds) In pictures, alpha helices are represented as spirals (purple ; left) and beta-pleated sheets as arrows (blue ; right)

Tertiary (3º) Structure The tertiary structure is the way the polypeptide chain coils and turns to form a complex molecular shape (i.e. the 3D shape) It is caused by interactions between R groups; including H-bonds, disulfide bridges, ionic bonds and hydrophobic interactions Relative amino acid positions are important (e.g. non-polar amino acids usually avoid exposure to aqueous solutions) Tertiary structure may be important for the function of the protein (e.g. specificity of active site in enzymes)

Quaternary (4º) Structure Multiple polypeptides or prosthetic groups may interact to form a single, larger, biologically active protein (quaternary structure) A prosthetic group is an inorganic compound involved in protein structure or function (e.g. the heme group in haemoglobin) A protein containing a prosthetic group is called a conjugated protein Quaternary structures may be held together by a variety of bonds (similar to tertiary structure)

7.3 U4 - Free ribosomes synthesize proteins for use primarily within the cell. AND 7.3 U5 - Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes. All proteins produced by eukaryotic cells are initially synthesised by ribosomes found freely circulating within the cytosol If the protein is targeted for intracellular use within the cytosol, the ribosome remains free and unattached If the protein is targeted for secretion, membrane fixation or use in lysosomes, the ribosome becomes bound to the ER

7.3 U4 - Free ribosomes synthesize proteins for use primarily within the cell. AND 7.3 U5 - Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes. Protein destination is determined by the presence or absence of an initial signal sequence on an adjascent polypeptide chain The presence of this signal sequence results in the recruitment of a signal recognition particle (SRP), which halts translation The SRP-ribosome complex then docks at a receptor located on the ER membrane (forming rough ER) Translation is re-initiated and the polypeptide chain continues to grow via a transport channel into the lumen of the ER The synthesised protein will then be transported via a vesicle to the Golgi complex (for secretion) or the lysosome Proteins targeted for membrane fixation (e.g. integral proteins) get embedded into the ER membrane The signal sequence is cleaved and the SRP recycled once the polypeptide is completely synthesised within the ER

Bibliography / Acknowledgments Bob Smullen